Hi Lori and Kevin: Thank you for your helpful responses! I was able to use "if (interactive()) { ... }" format and return the appDir object for the user. Thanks again!
Lindsay On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE <kevinru...@gmail.com> wrote: > > Hi Lindsay, > > Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R function > "iSEE" for an example of both the function return value, and the man page. > > First, I would suggest that your function _returns_ the "appDir" object to > the user, and that you leave it to the user to call "shiny::runApp" with > options appropriate to their system or preferences (e.g launch.browser=FALSE, > port=1234, etc). > > Second, for the man page, you don't have to put the _entire_ @example block > inside \dontrun{}. You can put everything that doesn't launch the Shiny app > outside the \dontrun{} block and only put the one "shiny" line inside the > \dontrun{}. The one line will represent less than 80% of the man page. > > However, even better, you can avoid the \dontrun{} option altogether and put > the "shiny" statement within a "if (interactive()) { ... }" block. > > So adapting you existing code, I would have > #' @examples > #' # Example 1: Create an interactive litre plot for the logged data using > #' # default background of hexagons. > #' > #' data(soybean_ir_sub) > #' data(soybean_ir_sub_metrics) > #' soybean_ir_sub_log <- soybean_ir_sub > #' soybean_ir_sub_log[,-1] <- log(soybean_ir_sub[,-1]+1) > #' if (interactive()){ > #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = > soybean_ir_sub_metrics) > #' } > #' > #' # Example 2: Repeat the same process, only now plot background data as > #' # individual points. Note this may be too slow now that all points are > drawn > #' # in the background. > #' if (interactive()){ > #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = > soybean_ir_sub_metrics, > #' option = "allPoints", pointColor = "red") > #' } > > However, once more, I suggest that you return "appDir", and you would then > have something like: > #' app <- plotLitreApp(data = soybean_ir_sub_log, dataMetrics = > soybean_ir_sub_metrics) > #' if (interactive()){ > #' shiny::runApp(app, [options defined by your user]) > #' } > > I hope this helps. Otherwise, let me know and I can chime in the review of > your package > > Best wishes > Kevin > > On Mon, Nov 19, 2018 at 7:00 PM Shepherd, Lori > <lori.sheph...@roswellpark.org> wrote: >> >> Submit with the dontrun{} and temporarily ignore the ERROR - when >> submitting please reference the explanation below. Your reviewer could >> provide more information and will decide how to proceed - generally >> examples will be run manually to check for accuracy and an exception can be >> made. >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> ________________________________ >> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of L Rutter >> <lindsayannerut...@gmail.com> >> Sent: Monday, November 19, 2018 1:49:50 PM >> To: bioc-devel@r-project.org >> Subject: [Bioc-devel] 80% of man pages must have runnable examples (package >> with numerous Shiny apps) >> >> Hello all: >> >> I am planning to submit a package to Bioconductor and have one last >> item from BiocCheck (error, warning, note) I have been unable to >> resolve: >> >> ERROR: At least 80% of man pages documenting exported objects must >> have runnable examples. The following pages do not: plotLitreApp.Rd, >> plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd >> >> I have 18 man pages (9 function-related, 8 data-related, and 1 >> package-related). Of these, 4 of the function-related man pages (the >> ones listed in the ERROR) are Shiny applications of the following >> format: >> >> appDir <- system.file("shiny-examples", "plotLitreApp", package = "bigPint") >> shiny::runApp(appDir, display.mode = "normal") >> >> If I do not have \dontrun{} around these shiny app examples, then R >> CMD check permanently halts on the "checking examples..." step. If I >> do have \dontrun{} around these shiny app examples, then R CMD >> BiocCheck gives me the error above. My question is: What is the >> recommended procedure in such a situation where the package is being >> prepared for Bioconductor submission? >> >> An example of one script causing the error can be found at: >> https://github.com/lrutter/bigPint/blob/master/R/plotLitreApp.R >> >> Thank you for any advice! >> Lindsay >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. 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